A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis

Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber
Chen, Nan, et al. "A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis." Computer physics communications 176.11 (2007): 670-681.
Publication Date: 
June, 2007

The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the size of simulations. In this paper we present a parallel CPM algorithm for simulations of morphogenesis, which includes cell–cell adhesion, a cell volume constraint, and cell haptotaxis. The algorithm uses appropriate data structures and checkerboard subgrids for parallelization. Communication and updating algorithms synchronize properties of cells simulated on different processor nodes. Tests show that the parallel algorithm has good scalability, permitting large-scale simulations of cell morphogenesis (107 or more cells) and broadening the scope of CPM applications. The new algorithm satisfies the balance condition, which is sufficient for convergence of the underlying Markov chain.